Publications by authors named "Shun Liu"

91 Publications

Taxonomy and Phylogeny of the Complex With Descriptions of Six New Species From East Asia.

Front Microbiol 2021 26;12:644979. Epub 2021 Mar 26.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.

is a common brown-rot fungal species found in northern hemisphere. It grows on many different gymnosperm and angiosperm trees. Recent studies show that it is a species complex; three species from North America and one species from Europe have been recognized in this complex. In the current study, six new species in the complex were discovered from East Asia, based on morphological characters and phylogenetic analyses inferred from the sequence data of the internal transcribed spacer (ITS) regions, the second subunit of RNA polymerase II (RPB2), and the translation elongation factor 1-α gene (TEF). Detailed descriptions of the six new species are provided. Our results also indicates that species of the complex from East Asia usually have limited distribution areas and host specialization.
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http://dx.doi.org/10.3389/fmicb.2021.644979DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8034269PMC
March 2021

Maternal overweight but not paternal overweight before pregnancy is associated with shorter newborn telomere length: evidence from Guangxi Zhuang birth cohort in China.

BMC Pregnancy Childbirth 2021 Apr 9;21(1):283. Epub 2021 Apr 9.

Department of Epidemiology and Health Statistics, School of Public Health, Guangxi Medical University, No. 22 Shuangyong Road, Nanning, 530021, Guangxi, China.

Background: Telomere length (TL) is variable at birth and is inversely associated with body mass index (BMI) in adulthood. A growing number of evidences suggested that a higher maternal pre-pregnancy BMI results in adverse offspring health outcomes, especially shorter newborn TL. However, a newborn's genetic endowment is equally derived from both parents, the association between parental pre-pregnancy BMI and newborn TL has been rarely discussed. We aimed to determine the association between parental pre-pregnancy BMI and newborn TL.

Methods: A total of 1082 parent-newborn pairs were recruited from the Guangxi Zhuang Birth Cohort (GZBC). TL in cord blood was measured using quantitative real-time polymerase chain reaction (qPCR) and expressed as the ratio of telomere copy number to single-copy gene number (T/S). A series of linear regressions were performed to assess the associations between parental pre-pregnancy BMI and newborn TL.

Results: Mothers who were overweight before pregnancy had significantly shorter cord blood telomere length in their newborns than those who were normal weight before pregnancy [percentage change: - 7.96% (95% CI: - 14.49 to - 0.69%; P = 0.032)]. Further analysis of the combined effects of parental weight status on newborn TL showed that TL was significantly shortened among newborns whose mothers were overweight and fathers were of healthy weight when compared with those whose mothers and fathers were both of normal weight [percentage change: - 8.38% (95% CI: - 15.47 to - 0.92%; P = 0.028)]. Subgroup analysis indicated these effects were more pronounced among male newborns and those whose paternal age < 31 years or maternal age ≥ 28 years at delivery.

Conclusions: Maternal pre-pregnancy overweight, but not paternal pre-pregnancy overweight is associated with shorter newborn TL. Weight control in reproductive women and effective healthy weight management before pregnancy may be of particular benefit for improving longevity and life quality of offspring.
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http://dx.doi.org/10.1186/s12884-021-03757-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8033662PMC
April 2021

Simultaneous determination of seven effective components in Shenkui Tongmai granules based on UHPLC-MS/MS.

J Pharm Pharmacol 2021 Mar 26. Epub 2021 Mar 26.

Department of Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, P.R China.

Objectives: The objective of the study was to establish the quality standard of the formulation of Shenkui Tongmai granules (SKTM) from the perspective of safety and effectiveness.

Methods: A sensitive and specific method to simultaneously detect seven effective components by ultra-high performance liquid chromatography-tandem-mass spectrometry (UHPLC-MS/MS) in SKTM, including calycosin 7-O-β-d-glucopyranoside, icariin, sodium danshensu, hyperoside, astragaloside IV, hesperidin, and salvianolic acid, was developed and validated. A Kromasil 100-3.5 C18 column with a mobile phase of 6.5 mmol/l ammonium acetate in acetonitrile was used to separate these above-listed components. Gradient programming was used with a flow rate of 0.2 ml/min, and the components were achieved in 13 min. Multiple reaction monitoring (MRM) in positive/negative mode was applied for the MS/MS detection.

Key Findings: The analytical method was satisfactorily validated for linearity, accuracy and precision, repeatability and stability. The developed UHPLC-MS/MS method had high repeatability and accuracy and it was in a good linear relationship within their respective ranges (r = 0.9999) with the RSD value of the sample recovery of less than 5%.

Conclusions: The current method established here is suitable for use in determining seven effective components in SKTM simultaneously, which may provide a new reliable method for overall quality control of SKTM.
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http://dx.doi.org/10.1093/jpp/rgab017DOI Listing
March 2021

Gut microbiota alterations associated with antibody-mediated rejection after kidney transplantation.

Appl Microbiol Biotechnol 2021 Mar 24;105(6):2473-2484. Epub 2021 Feb 24.

Department of Urology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, China.

Antibody-mediated rejection (AMR) has become the major challenge for kidney transplantation, and the efficacy of existing therapies was limited to prevent AMR. Increasing evidences have demonstrated the link between gut microbiota alterations and allograft outcome. However, there has been no comprehensive analysis to profile the gut microbiota associated with AMR after kidney transplantation. We performed this study to characterize the gut microbiota possibly associated with AMR. Fecal specimens were collected from 24 kidney transplantation recipients with AMR and 29 controls. DNA extracted from the specimens was processed for 16S rRNA gene sequencing using Illumina MiSeq. Gut microbial community of recipients with AMR was significantly different from that of controls based on unweighted (P = 0.001) and weighted (P = 0.02) UniFrac distances, and the bacterial richness (observed species: P = 0.0448; Chao1 index: P = 0.0450; ACE index: P = 0.0331) significantly decreased in the AMR group. LEfSe showed that 1 phylum, 5 classes, 7 families, and 10 genera were increased, whereas 1 class, 2 order, 3 families, and 4 genera were decreased in the AMR group. Specific taxa such as Clostridiales could be potentially used as biomarkers to distinguish the recipients with AMR from the controls (AUC = 0.77). PICRUSt analysis illustrated that 16 functional pathways were with significantly different abundances in the AMR and control groups. Our findings provide a foundation for further investigation on the role of gut microbiota in AMR after kidney transplantation, and potentially support novel diagnostic biomarkers and therapeutic options for AMR. KEY POINTS: • Gut microbial community of kidney recipients with AMR was different from that of controls. • Clostridiales is a potential marker to distinguish recipients with AMR from controls.
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http://dx.doi.org/10.1007/s00253-020-11069-xDOI Listing
March 2021

Species Diversity and Molecular Phylogeny of (Polyporales, Basidiomycota).

Front Microbiol 2021 4;12:631166. Epub 2021 Feb 4.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.

is a cosmopolitan brown-rot fungal genus, recognizable by blue-tinted basidiocarps. Species in this genus were usually treated as belonging to the complex, however, recent phylogenetic analyses showed that this complex represents an independent genus. During further studies on , five new species were discovered based on morphological features and molecular data. Phylogenetic analyses of were conducted using the internal transcribed spacer (ITS) regions, the large subunit of nuclear ribosomal RNA gene (nLSU), the small subunit of nuclear ribosomal RNA gene (nSSU), the small subunit of mitochondrial rRNA gene (mtSSU), the largest subunit of RNA polymerase II (RPB1), the second largest subunit of RNA polymerase II (RPB2), and the translation elongation factor 1-α gene (TEF); illustrated descriptions of the new species are provided. In addition, fifteen species previously belonging to the complex are transferred to and proposed as new combinations.
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http://dx.doi.org/10.3389/fmicb.2021.631166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7889604PMC
February 2021

Postoperative hypothermia after total aortic arch replacement in acute type A aortic dissection-multivariate analysis and risk identification for postoperative hypothermia occurrence.

J Thorac Dis 2020 Dec;12(12):7089-7096

Department of Cardiovascular Surgery, Zhongshan Hospital, Shanghai Cardiovascular Institution, Fudan University, Shanghai, China.

Background: Postoperative hypothermia (PH) is a common physiological abnormality associated with increased morbidity and mortality after non-cardiac surgery. The incidence, risk factors of PH and its impact on early outcomes after total aortic arch replacement are not clear.

Methods: We conducted a retrospective cohort study in patients with acute type A aortic dissection who underwent total arch replacement from January 2013 to December 2016 at our institution. Basic variables, procedural and postoperative early outcomes were collected. Univariate and multivariate statistical analysis were performed for statistical interpretation. The early outcomes were compared between patients with or without PH.

Results: A total of 300 patients (age 53.8±11.5 years, female 63, 21.0%) with acute type A aortic dissection underwent total arch replacement. Forty-four patients (14.7%) developed PH. The independent risk factors of PH are age and the intraoperative lowest bladder temperature. There is no significant difference in major postoperative morbidity and mortality between patients with or without PH.

Conclusions: The incidence of PH after total arch replacement in acute type A aortic dissection is relatively low. The independent risk factors of PH in this population include age and the intraoperative lowest bladder temperature. With comprehensive rewarming strategy upon arrival at the ICU, the PH is easy to be corrected, and the adverse effect of transient PH on early outcomes after arch surgery is minimal.
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http://dx.doi.org/10.21037/jtd-20-1709DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7797820PMC
December 2020

The pollution halo effect of technology spillover and pollution haven effect of economic growth in agricultural foreign trade: two sides of the same coin?

Environ Sci Pollut Res Int 2021 Jan 6. Epub 2021 Jan 6.

College of Tourism, Hunan Normal University, Changsha, 410081, China.

The existing literature on the environmental Kuznets curve (EKC) fails to investigate the spatial attribute of the "pollution halo" effect or to integrate the "pollution haven" effect. This paper extends the EKC model to the spatial Durbin model by exploring the spatial spillover of disembodied technology and the pollution transfer effect of environmental regulation. Taking Chinese agricultural foreign trade as an example, our paper finds that the technology spillover does not bring a pollution halo effect to local areas but to adjacent areas. The pollution haven effect impacts the EKC's turning point, which can be divided into two curves in the spatial dimension: an inverted U-shaped curve, in which the turning point represents the effect of technological innovation, and a U-shaped curve, in which the turning point represents the transfer effect of pollution-intensive industries. Based on the conclusion, this paper recommends that agricultural non-point pollution reduction should be nationally coordinated to establish transport infrastructure and the agricultural human capital conditions for the spatial diffusion of disembodied technology.
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http://dx.doi.org/10.1007/s11356-020-11786-wDOI Listing
January 2021

A method of railway system safety analysis based on cusp catastrophe model.

Accid Anal Prev 2021 Mar 29;151:105935. Epub 2020 Dec 29.

Department of Electrical Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region. Electronic address:

For rail transit systems, safety is one of the most important goals that need to be guaranteed. We build a method of railway system safety analysis based on the cusp catastrophe model. This method describes the continuous changing process of railway system safety and considers the emergent property of safety. This method solves the problem that the outputs of most static analysis methods of railway system safety do not have continuity and avoids the complex analysis process and heavy computation burden brought by using some dynamic models such as state transition models. The quantitative case study of the continuous changing process of system safety in the evolution process of the Yong-Wen railway accident shows that the visualized outputs obtained by using this method are consistent with the actual situation. This method has the potential to be applied in the real-time monitoring of railway system safety and the early warning of train accidents.
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http://dx.doi.org/10.1016/j.aap.2020.105935DOI Listing
March 2021

ColorCells: a database of expression, classification and functions of lncRNAs in single cells.

Brief Bioinform 2020 Dec 14. Epub 2020 Dec 14.

Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P. R. China.

Although long noncoding RNAs (lncRNAs) have significant tissue specificity, their expression and variability in single cells remain unclear. Here, we developed ColorCells (http://rna.sysu.edu.cn/colorcells/), a resource for comparative analysis of lncRNAs expression, classification and functions in single-cell RNA-Seq data. ColorCells was applied to 167 913 publicly available scRNA-Seq datasets from six species, and identified a batch of cell-specific lncRNAs. These lncRNAs show surprising levels of expression variability between different cell clusters, and has the comparable cell classification ability as known marker genes. Cell-specific lncRNAs have been identified and further validated by in vitro experiments. We found that lncRNAs are typically co-expressed with the mRNAs in the same cell cluster, which can be used to uncover lncRNAs' functions. Our study emphasizes the need to uncover lncRNAs in all cell types and shows the power of lncRNAs as novel marker genes at single cell resolution.
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http://dx.doi.org/10.1093/bib/bbaa325DOI Listing
December 2020

Minimally invasive valve replacement for late tricuspid regurgitation after left-sided valve surgery.

Ann Thorac Surg 2020 Nov 17. Epub 2020 Nov 17.

Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Engineering Research Center of Heart Valve, Shanghai, China; Shanghai Institute of Cardiovascular Disease, Shanghai, China. Electronic address:

Late severe tricuspid regurgitation after left-sided valve surgery can negatively affect long-term prognosis and quality of life. Because of extensive trauma and poor right heart function, perioperative mortality after reoperation for tricuspid regurgitation historically remained high. To its end, multiple minimally invasive techniques were adopted at our center recently, including endoscopy-assist right minithoracotomy, vacuum-assist single femoral venous drainage without dissecting or snaring vena cava, direct right atriotomy through pericardium and the beating-heart technique. Moreover, the tricuspid valves were replaced with bioprostheses in majority of those patients at our center. The mid-term outcomes of minimally invasive bioprosthetic replacement were favorable.
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http://dx.doi.org/10.1016/j.athoracsur.2020.08.091DOI Listing
November 2020

Stabilization of ERK-Phosphorylated METTL3 by USP5 Increases mA Methylation.

Mol Cell 2020 11;80(4):633-647.e7

Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA. Electronic address:

N-methyladenosine (mA) is the most abundant mRNA modification and is installed by the METTL3-METTL14-WTAP methyltransferase complex. Although the importance of mA methylation in mRNA metabolism has been well documented recently, regulation of the mA machinery remains obscure. Through a genome-wide CRISPR screen, we identify the ERK pathway and USP5 as positive regulators of the mA deposition. We find that ERK phosphorylates METTL3 at S43/S50/S525 and WTAP at S306/S341, followed by deubiquitination by USP5, resulting in stabilization of the mA methyltransferase complex. Lack of METTL3/WTAP phosphorylation reduces decay of mA-labeled pluripotent factor transcripts and traps mouse embryonic stem cells in the pluripotent state. The same phosphorylation can also be found in ERK-activated human cancer cells and contribute to tumorigenesis. Our study reveals an unrecognized function of ERK in regulating mA methylation.
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http://dx.doi.org/10.1016/j.molcel.2020.10.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7720844PMC
November 2020

Pulmonary valve replacement in primary repair of tetralogy of Fallot in adult patients.

J Thorac Dis 2020 Sep;12(9):4833-4841

Department of Cardiovascular Surgery, Zhongshan Hospital, Shanghai Cardiovascular Institution, Fudan University, Shanghai, China.

Background: Adults with unrepaired tetralogy of Fallot (ToF) are common in developing countries. Long-term overload of the right ventricle places adult patients at risk for postoperative right heart failure after primary repair, which contributes to morbidity and mortality. The effect of pulmonary valve replacement (PVR) in reducing postoperative morbidity and mortality in adults has never been validated.

Methods: We conducted a retrospective cohort study in adults (age ≥18 years) with ToF undergoing primary repair from January 2014 to December 2019 at our institution. Patients were divided into three groups according to techniques used to enlarge the right ventricle outflow tract (RVOT). Baseline variables and perioperative outcomes were collected. The primary endpoint was operative mortality. Secondary endpoints were incidences of right heart failure and stage 3 acute kidney injury (AKI).

Results: A total of 56 patients were enrolled (mean age 41.5±11.7 years, 30 females, 53.6%). They were divided into three groups designated as the following: TA-PVR group for trans-annular patch enlargement with PVR; TA group for trans-annulus patch enlargement without PVR; and group AP for annulus preservation. Four patients (7.1%) died postoperatively, all due to right heart failure. All twelve patients in the TA-PVR group survived. There was no significant difference in mortalities among groups. Ten patients (17.9%) developed right heart failure after surgery with no significant difference among groups. Three patients (5.4%) developed stage 3 AKI after surgery, none belonging to the TA-PVR group, however, not statistically significant.

Conclusions: Right heart failure is a common complication after primary repair of adult ToF. Trans-annulus patch enlargement should be cautiously selected in this population. PVR with trans-annulus patch enlargement may be a promising technique to protect against postoperative right heart failure and mortality when annulus preservation is not feasible.
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http://dx.doi.org/10.21037/jtd-20-1475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7578467PMC
September 2020

Quantifying the learning curve of emergent total arch replacement in acute type A aortic dissection.

J Thorac Dis 2020 Aug;12(8):4070-4081

Department of Cardiovascular Surgery, Zhongshan Hospital, Shanghai Cardiovascular Institution, Fudan University, Shanghai, China.

Background: Acute type A aortic dissection with arch involvement is a life-threatening condition, which requires immediate surgical attention. Emergent total arch replacement and root reconstruction is a technically demanding operation with varying outcomes based on surgeon experience. The human factors in total arch replacement in the emergent setting have never been systematically investigated. The ability of surgeons with low volumes to achieve acceptable results in their start-up period is not known.

Methods: From January 2013 to December 2016, patients with acute type A aortic dissection who underwent emergent total arch replacement with three surgeons were enrolled. Basic characteristics, procedural and postoperative outcomes were collected. The time of critical surgical steps and operative mortality were calculated using descriptive statistics and cumulative SUM (CUSUM) analysis.

Results: A total of 300 patients (age 53.8±11.5 years, female 63, 21.0%) with acute type A aortic dissection underwent emergent total arch replacement. A total of 219 patients (73.0%) had root reinforcement, 295 patients (98.3%) underwent frozen elephant trunk repair. Mean circulatory arrest and cross-clamp times were 29.8±9.8 and 112.3±32.1 min, respectively. The operative mortality was 6.7%, the stroke rate was 4.0%. The mean length of postoperative ICU and hospital stays were 8.4±10.6 and 18.0±12.2 days, respectively. By CUSUM depictions, surgeons appeared to have different learning curves with regards to operative time. By CUSUM failure analysis on operative mortality, two newly appointed surgeons in their start-up period stayed in an acceptable range, while one senior surgeon with higher volumes experienced superior outcomes and better performance.

Conclusions: Although emergent total arch replacement for acute type A dissection is a complex scenario, surgeons well-trained in adult cardiac surgery are able to achieve acceptable results in their start-up period.
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http://dx.doi.org/10.21037/jtd-20-912DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7475536PMC
August 2020

Photosynthetic capacity of male and female Hippophae rhamnoides plants along an elevation gradient in eastern Qinghai-Tibetan Plateau, China.

Tree Physiol 2021 01;41(1):76-88

Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China.

Elevational variations in the growing environment and sex differences in individuals drive the diversification of photosynthetic capacity of plants. However, photosynthetic response of dioecious plants to elevation gradients and the mechanisms that cause these responses are poorly understood. We measured foliar gas exchange, chlorophyll fluorescence and nitrogen allocations of male and female Seabuckthorn (Hippophae rhamnoides L.) at the elevation of 1900-3700 m above sea level (a.s.l.) on the eastern Qinghai-Tibetan Plateau, China. Male and female plants showed increased leaf photosynthetic capacity at higher elevation generally with no sex-specific difference. Photosynthetic photon flux density-saturated photosynthesis (Asat) was limited mostly by diffusional components (77 ± 1%), whereas biochemical components contributed minor limitations (22 ± 1%). Mesophyll conductance (gm) played an essential role in Asat variation, accounting for 40 ± 2% of the total photosynthetic limitations and had a significant positive correlation with Asat. Leaf nitrogen allocations to Rubisco (PR) and bioenergetics (PB) in the photosynthetic apparatus were major drivers for variations in photosynthetic nitrogen-use efficiency. The increase of these resource uptake capacities enables H. rhamnoides to maintain a high level of carbon assimilation and function efficiently to cope with the harsh conditions and shorter growing season at higher elevation.
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http://dx.doi.org/10.1093/treephys/tpaa105DOI Listing
January 2021

An non-loglinear enzyme-driven law of photosynthetic scaling in two representative crop seedlings under different water conditions.

Sci Rep 2020 07 29;10(1):12720. Epub 2020 Jul 29.

College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China.

The loglinear pattern of respiratory scaling has been studied for over a century, while an increasing number of non-loglinear patterns have been found in the plant kingdom. Several previous studies had attempted to reconcile conflicting patterns from the aspects of statistical approaches and developmental stages of the organisms. However, the underlying enzymatic mechanism was largely ignored. Here, we propose an enzyme-driven law of photosynthetic scaling and test it in typical crop seedlings under different water conditions. The results showed that the key enzyme activity, the relative photosynthetic assimilation and the relative growth rate were all constrained by the available water, and the relationship between these biological traits and the available water supported our predictions. The enzyme-driven law appears to be more suitable to explain the curvature of photosynthetic scaling than the well-established power law, since it provides insight into the biochemical origin of photosynthetic assimilation.
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http://dx.doi.org/10.1038/s41598-020-69702-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7391708PMC
July 2020

Treatment Efficacy of Chuang Ling Ye, a Traditional Chinese Herbal Medicine Compound, on Idiopathic Granulomatous Mastitis: A Randomized Controlled Trial.

Evid Based Complement Alternat Med 2020 29;2020:6964801. Epub 2020 Jun 29.

Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China.

Objective: To explore whether Chuang Ling Ye (CLY), a traditional Chinese herbal medicine compound, could improve the treatment of idiopathic granulomatous mastitis (IGM) via decreasing inflammatory response.

Methods: Herein, 40 patients with IGM who had wounds requiring dressing change were enrolled and randomly divided into two groups: the CLY group and the control group. The size of the neoplasm and pain score of patients were followed-up for 4 weeks. Local tissues were taken during dressing change and examined by commercial enzyme-linked immunosorbent assay (ELISA) kits. The levels of inflammatory markers, including interleukin-1 (IL-1), IL-2, IL-6, interferon gamma (IFN-), and tumor necrosis factor- (TNF-) were measured.

Results: After treatment, the size of the neoplasm in the CLY group was significantly smaller than that in the control group (14.28 cm ± 8.96 cm vs. 21.14 cm ± 0.12 cm, =0.038), and the pain scores were markedly reduced (=0.004). Besides, CLY downregulated the expression levels of IL-1, IFN-, and TNF-.

Conclusion: External use of CLY could reduce the neoplasm of IGM by inhibiting local inflammation. This trial is registered with ChiCTR1800017744.
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http://dx.doi.org/10.1155/2020/6964801DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7341429PMC
June 2020

Big Data-Based Identification of Multi-Gene Prognostic Signatures in Liver Cancer.

Front Oncol 2020 28;10:847. Epub 2020 May 28.

School of Public Health, Guangxi Medical University, Nanning, China.

Simultaneous identification of multiple single genes and multi-gene prognostic signatures with higher efficacy in liver cancer has rarely been reported. Here, 1,173 genes potentially related to the liver cancer prognosis were mined with Coremine, and the gene expression and survival data in 370 samples for overall survival (OS) and 319 samples for disease-free survival (DFS) were retrieved from The Cancer Genome Atlas. Numerous survival analyses results revealed that 39 genes and 28 genes significantly associated with DFS and OS in liver cancer, including 18 and 12 novel genes that have not been systematically reported in relation to the liver cancer prognosis, respectively. Next, totally 9,139 three-gene combinations (including 816 constructed by 18 novel genes) for predicting DFS and 3,276 three-gene combinations (including 220 constructed by 12 novel genes) for predicting OS were constructed based on the above genes, and the top 15 of these four parts three-gene combinations were selected and shown. Moreover, a huge difference between high and low expression group of these three-gene combination was detected, with median survival difference of DFS up to 65.01 months, and of OS up to 83.57 months. The high or low expression group of these three-gene combinations can predict the longest prognosis of DFS and OS is 71.91 months and 102.66 months, and the shortest is 6.24 months and 13.96 months. Quantitative real-time polymerase chain reaction and immunohistochemistry reconfirmed that three genes , and contained in one of the above combinations, are significantly dysregulated in liver cancer tissues, low expression of , and is associated with poor prognosis in liver cancer. Overall, we discovered a few novel single genes and multi-gene combinations biomarkers that are closely related to the long-term prognosis of liver cancer, and they can be potential therapeutic targets for liver cancer.
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http://dx.doi.org/10.3389/fonc.2020.00847DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7270198PMC
May 2020

Influence of different acoustic cues in L1 lexical tone on the perception of L2 lexical stress using principal component analysis: an ERP study.

Exp Brain Res 2020 Jun 20;238(6):1489-1498. Epub 2020 May 20.

Faculty of Education, University of Macau, Macau, China.

Previous studies have widely explored the prosodic transfer from L1 to L2 during speech perception across stress languages. However, few if any studies have investigated the transfer from L1 tonal language to L2 stress language and the relative roles of different acoustic cues underlying the transfer. Therefore, the current study was conducted to compare the perception of English lexical stress between Mandarin and Cantonese speakers who learn English as a foreign language. The event-related potential measurements and the principal component analysis were conducted for the two groups to explore the roles of different acoustic cues in the perception of English speech. The results demonstrated that compared with the Mandarin group, the Cantonese speakers relied more on pitch information and the reliance holds even when all the three cues varied simultaneously. Therefore, it was concluded that prosodic transfer from L1 lexical tone to L2 lexical stress occurred at the acoustic level, and the native linguistic background shaped the manner how speakers perceived the L2 speech.
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http://dx.doi.org/10.1007/s00221-020-05823-wDOI Listing
June 2020

Identification of Leg Chemosensory Genes and Sensilla in the .

Front Physiol 2020 15;11:276. Epub 2020 Apr 15.

State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.

(Hemiptera: Miridae), one of the main insect pests, causes severe damage in cotton and many other economic crops. As is well-known, legs play important roles in the chemoreception of insects. In this study, the putative chemosensory proteins in legs of involved in close or contact chemical communication of adult bugs were investigated using RNA transcriptome sequencing and qPCR methods. Transcriptome data of forelegs, middle legs and hind legs of adult bugs demonstrated that 20 odorant binding protein (OBP) genes, eight chemosensory protein (CSP) genes, one odorant receptor (OR) gene, one ionotropic receptor (IR) gene and one sensory neuron membrane protein (SNMP) gene were identified in legs of . Compared to the previous antennae transcriptome data, five CSPs, IR21a and SNMP2a were newly identified in legs. Results of qPCR analysis indicated that all these putative chemosensory genes were ubiquitously expressed in forelegs, middle legs and hind legs of bugs. Furthermore, four types of sensilla on legs of including sensilla trichodea (subtypes: long straight sensilla trichodea, Str1; long curved sensilla trichodea, Str2), sensilla chaetica (subtypes: sensilla chaetica 1, Sch1; sensilla chaetica 2, Sch2; and sensilla chaetica 3, Sch3), sensilla basiconca (subtypes: medium-long sensilla basiconca, Sba1; short sensilla basiconca, Sba2) and Böhm bristles (BB) were found using scanning electron microscopy. Additionally, the largest number of sensilla was observed on hind legs, while the forelegs had the smallest number of sensilla. Our data provide valuable insights into understanding the chemoreception of legs in
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http://dx.doi.org/10.3389/fphys.2020.00276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7174674PMC
April 2020

REPIC: a database for exploring the N-methyladenosine methylome.

Genome Biol 2020 04 28;21(1):100. Epub 2020 Apr 28.

Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.

The REPIC (RNA EPItranscriptome Collection) database records about 10 million peaks called from publicly available mA-seq and MeRIP-seq data using our unified pipeline. These data were collected from 672 samples of 49 studies, covering 61 cell lines or tissues in 11 organisms. REPIC allows users to query N-methyladenosine (mA) modification sites by specific cell lines or tissue types. In addition, it integrates mA/MeRIP-seq data with 1418 histone ChIP-seq and 118 DNase-seq data tracks from the ENCODE project in a modern genome browser to present a comprehensive atlas of mA methylation sites, histone modification sites, and chromatin accessibility regions. REPIC is accessible at https://repicmod.uchicago.edu/repic.
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http://dx.doi.org/10.1186/s13059-020-02012-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7187508PMC
April 2020

Transapical transcatheter aortic valve implantation for predominant aortic regurgitation with a self-expandable valve.

J Thorac Dis 2020 Mar;12(3):538-549

Department of Cardiovascular Surgery, Zhongshan Hospital, Shanghai Cardiovascular Institution, Fudan University, Shanghai 200032, China.

Background: Transcatheter aortic valve implantation (TAVI) has become the gold standard for high-risk severe aortic stenosis. However, the experience of treating aortic regurgitation (AR) with this technology is still limited. Previously, we have demonstrated excellent 1-year outcomes of transapical TAVI with J-Valve (JieCheng Medical Technology Co., Ltd., Suzhou, China) in treating predominant AR, while the mid-term outcomes up to 4 years have never been reported.

Methods: Transapical TAVI with J-Valve to treat predominant AR was performed in 47 patients in Zhongshan Hospital from May 2014 through October 2018. Procedural and clinical outcomes with follow-up up to 4 years were analyzed using Valve Academic Research Consortium-2 criteria (VARC-2).

Results: All patients (age 73.7±7.9 years) were considered to be prohibitive or high-risk for surgical aortic valve replacement (SAVR) (logistic European System for Cardiac Operative Risk Evaluation, 21.1% to 44.4%; mean, 24.3%±5.1%) after evaluated by a multidisciplinary heart team. Transapical implantations were successful in all patients. The clinical outcomes of the entire cohort in the latest follow-up (371 to 1,968 days, median 574 days) included all-cause mortality (6.4%), disabling stroke (2.3%), new permanent pacemaker (6.8%) and valve-related re-intervention (0). Paravalvular leak (PVL) was rate as none or trace in 37 of 44 and mild in 7 of 44 patients at the latest follow-up. Mean transvalvular gradient was favorable after valve implantation during follow-up at 9.3±2.5 mmHg.

Conclusions: This study revealed that, transapical TAVI with J-Valve for treating AR has encouraging mid-term outcomes, and the advantages at one year demonstrated in previous study can be maintained through 4 years.
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http://dx.doi.org/10.21037/jtd.2020.01.04DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7139073PMC
March 2020

Lats1/2 Sustain Intestinal Stem Cells and Wnt Activation through TEAD-Dependent and Independent Transcription.

Cell Stem Cell 2020 05 6;26(5):675-692.e8. Epub 2020 Apr 6.

Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA. Electronic address:

Intestinal homeostasis is tightly regulated by complex yet poorly understood signaling networks. Here, we demonstrate that Lats1/2, the core Hippo kinases, are essential to maintain Wnt pathway activity and intestinal stem cells. Lats1/2 deletion leads to loss of intestinal stem cells but drives Wnt-uncoupled crypt expansion. To explore the function of downstream transcriptional enhanced associate domain (TEAD) transcription factors, we identified a selective small-molecule reversible inhibitor of TEAD auto-palmitoylation that directly occupies its lipid-binding site and inhibits TEAD-mediated transcription in vivo. Combining this chemical tool with genetic and proteomics approaches, we show that intestinal Wnt inhibition by Lats deletion is Yes-associated protein (YAP)/transcriptional activator with PDZ-binding domain (TAZ) dependent but TEAD independent. Mechanistically, nuclear YAP/TAZ interact with Groucho/Transducin-Like Enhancer of Split (TLE) to block Wnt/T-cell factor (TCF)-mediated transcription, and dual inhibition of TEAD and Lats suppresses Wnt-uncoupled Myc upregulation and epithelial over-proliferation in Adenomatous polyposis coli (APC)-mutated intestine. Our studies highlight a pharmacological approach to inhibit TEAD palmitoylation and have important implications for targeting Wnt and Hippo signaling in human malignancies.
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http://dx.doi.org/10.1016/j.stem.2020.03.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310193PMC
May 2020

Association of prenatal exposure to bisphenols and birth size in Zhuang ethnic newborns.

Chemosphere 2020 Aug 4;252:126422. Epub 2020 Mar 4.

Department of Epidemiology and Health Statistics, School of Public Health, Guangxi Medical University, Nanning, 530021, Guangxi, China. Electronic address:

Prenatal exposure to bisphenol A (BPA) and its analogues can affect fetal growth and development. However, epidemiologic findings were inconsistent and there was a lack of study for BPA analogues. We aimed to examine the associations between prenatal exposure to BPA, bisphenol B (BPB), bisphenol F (BPF), bisphenol S (BPS), and tetrabromobisphenol A (TBBPA) and birth size. 2023 mother-infant pairs were included in this study. The associations between serum bisphenol levels and birth size were analyzed by multivariate linear regression models. After adjusting for covariates, one log10-unit increase in serum BPA was correlated with a 32.10 g (95% CI: -61.10, -3.10) decrease in birth weight for all infants, and the inverse association was only observed in males when stratified analysis by gender. Additionally, higher BPF concentrations were associated with decreasing birth weight (P for trend = 0.031), ponderal index (P for trend = 0.021), and birth weight Z-scores (P for trend = 0.039) in all infants, and the inverse associations were also only observed in males when stratified analysis by gender. Similarly, higher TBBPA levels were also correlated with decreased birth weight (P for trend = 0.023). However, after gender stratification, higher TBBPA concentrations were associated with a decrease in birth weight (P for trend = 0.007), birth length (P for trend = 0.026), and birth weight Z-scores (P for trend = 0.039) in males. Our data suggested an inverse association of prenatal exposure to BPA, BPF, and TBBPA and birth size, which may be more pronounced in male infants.
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http://dx.doi.org/10.1016/j.chemosphere.2020.126422DOI Listing
August 2020

LINC02499, a novel liver-specific long non-coding RNA with potential diagnostic and prognostic value, inhibits hepatocellular carcinoma cell proliferation, migration, and invasion.

Hepatol Res 2020 Jun 2;50(6):726-740. Epub 2020 Mar 2.

Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, China.

Aim: Liver-specific non-coding RNAs have been reported to play crucial roles in hepatocellular carcinoma (HCC). We investigated the possible biological performance of a novel liver-specific long non-coding RNA, LINC02499, in HCC.

Methods: The association between LINC02499 expression and HCC was evaluated based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, and then confirmed in a HCC cohort by quantitative real-time polymerase chain reaction. The effects of LINC02499 on HCC cells were verified by gain- and loss-of-function assays. Pathway enrichment analyses were used to explore the potential mechanism of LINC02499 in HCC.

Results: LINC02499 expression was remarkably decreased in HCC tissues compared to adjacent non-tumor tissues based on TCGA (P < 0.001) and GEO databases (P < 0.001) and our HCC cohort (P < 0.001). Decreased LINC02499 was also significantly associated with poorer overall survival in both the TCGA database (P = 0.009) and our HCC cohort (P = 0.002). Furthermore, the receiver operating characteristic analysis indicated that LINC02499 showed a good performance in HCC diagnosis (area under the curve = 0.879, P < 0.001), and both sensitivity and specificity were 83.8%. In addition, up- and downregulated LINC02499 significantly impacted proliferation, migration, and invasion abilities of HCC cells in vitro. Pathway enrichment analyses revealed that the potential target genes of LINC02499 were involved in "Complement and coagulation cascades" and "Butanoate metabolism" pathways.

Conclusion: LINC02499 could be a potential novel diagnostic and prognostic biomarker for HCC patients, and it could exert a tumor suppressor role in the progression of HCC.
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http://dx.doi.org/10.1111/hepr.13491DOI Listing
June 2020

Preventable lifestyle and eating habits associated with gastric adenocarcinoma: A case-control study.

J Cancer 2020 1;11(5):1231-1239. Epub 2020 Jan 1.

Department of General Surgery, the First Affiliated Hospital of Anhui Medical University.

Besides the well-established risk factors for gastric adenocarcinoma (GaC), many other etiological factors remain largely unexplored. This large comprehensive case-control study aimed to investigate the preventable lifestyle and eating habits associated with GaC. Consecutive patients with primary microscopically-confirmed GaC diagnosed in 2016-2018 were matched by sex, age, height, and socioeconomic status at a 1:1 ratio with healthy controls. Association of GaC versus control with investigated factors was assessed using the multivariable-adjusted conditional logistic regression for paired samples. Together 302 GaC patients and 302 healthy controls were investigated. Participants receiving higher education and those eating majorly vegetables had less frequently GaC. The majorly frying cooking habit was associated with a higher incidence of GaC. People complaining about poor sleep quality had more often GaC. The more often one smoked, the more often he/she had GaC. A higher frequency for having pickled food was associated with more frequent GaC, while having more frequently vegetables/fruit, beans, or kelps was associated with less often GaC. A greater preference for sour or bitter taste was associated with less frequent GaC. The frequencies of thin liquid intake after meal, swallowing hot food without adequate cooling, doing other things while eating, eating overnight food, and eating midnight snack were all positively associated with GaC, while going to bed regularly was associated with less often GaC. Education level, sleep quality, smoking, the frequencies of use of several foods and seasonings, the preference for specific tastes, and various eating and living habits were associated with GaC. The findings offer important hints for further prospective investigations and for easy effective GaC-preventative strategy-making.
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http://dx.doi.org/10.7150/jca.39023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6959061PMC
January 2020

PI signal transduction and ubiquitination respond to dehydration stress in the red seaweed Gloiopeltis furcata under successive tidal cycles.

BMC Plant Biol 2019 Nov 27;19(1):516. Epub 2019 Nov 27.

Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.

Background: Intermittent dehydration caused by tidal changes is one of the most important abiotic factors that intertidal seaweeds must cope with in order to retain normal growth and reproduction. However, the underlying molecular mechanisms for the adaptation of red seaweeds to repeated dehydration-rehydration cycles remain poorly understood.

Results: We chose the red seaweed Gloiopeltis furcata as a model and simulated natural tidal changes with two consecutive dehydration-rehydration cycles occurring over 24 h in order to gain insight into key molecular pathways and regulation of genes which are associated with dehydration tolerance. Transcription sequencing assembled 32,681 uni-genes (GC content = 55.32%), of which 12,813 were annotated. Weighted gene co-expression network analysis (WGCNA) divided all transcripts into 20 modules, with Coral2 identified as the key module anchoring dehydration-induced genes. Pathways enriched analysis indicated that the ubiquitin-mediated proteolysis pathway (UPP) and phosphatidylinositol (PI) signaling system were crucial for a successful response in G. furcata. Network-establishing and quantitative reverse transcription PCR (qRT-PCR) suggested that genes encoding ubiquitin-protein ligase E3 (E3-1), SUMO-activating enzyme sub-unit 2 (SAE2), calmodulin (CaM) and inositol-1,3,4-trisphosphate 5/6-kinase (ITPK) were the hub genes which responded positively to two successive dehydration treatments. Network-based interactions with hub genes indicated that transcription factor (e.g. TFIID), RNA modification (e.g. DEAH) and osmotic adjustment (e.g. MIP, ABC1, Bam1) were related to these two pathways.

Conclusions: RNA sequencing-based evidence from G. furcata enriched the informational database for intertidal red seaweeds which face periodic dehydration stress during the low tide period. This provided insights into an increased understanding of how ubiquitin-mediated proteolysis and the phosphatidylinositol signaling system help seaweeds responding to dehydration-rehydration cycles.
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http://dx.doi.org/10.1186/s12870-019-2125-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6880600PMC
November 2019

gen. nov. (Polyporaceae, Basidiomycota) evidenced by morphological characters and phylogenetic analyses with descriptions of four new species.

MycoKeys 2019 21;57:61-84. Epub 2019 Aug 21.

Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China Beijing Forestry University Beijing China.

A new poroid wood-inhabiting fungal genus, gen. nov., is proposed on the basis of morphological characters and molecular evidence. The genus is characterized by an annual growth habit, effused-reflexed to pileate basidiocarps with pale yellowish brown to yellowish brown, concentrically zonate or sulcate, and velutinate pileal surface, a trimitic hyphal system with clamped generative hyphae, tissues turning to dark in KOH, oblong to broadly ellipsoid, hyaline, smooth, and slightly thick-walled basidiospores. Phylogenetic analysis based on ITS+nLSU sequences indicate that belongs to the core polyporoid clade. The combined ITS+nLSU+mtSSU+EF1-α+RPB2 sequences dataset of representative taxa in the Polyporaceae demonstrate that is grouped with but forms a monophyletic lineage. In addition, four new species of , , , , and are described.
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http://dx.doi.org/10.3897/mycokeys.57.38035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6713667PMC
August 2019

Indirect effects of water availability in driving and predicting productivity in the Gobi desert.

Sci Total Environ 2019 Dec 17;697:133952. Epub 2019 Aug 17.

College of Life Sciences, Zhejiang University, Hangzhou 310058, China. Electronic address:

Climate is the fundamental determinant of plant metabolism and net primary productivity (NPP). However, whether climate drives NPP directly or indirectly is not well understand. The Gobi desert across a precipitation gradient in the arid zone provides an ideal naturally-controlled platform for studying the precipitation-productivity relationships. We conducted 3-year experiments in four Gobi desert shrublands across an aridity gradient in Gansu Province of China to test the relationship between water availability and shrub productivity as well as the relative importance of the possible factors driving productivity (using piecewise structural equation modeling) and to explore the appropriate variables for predicting productivity (using three spatial models). The results showed that water availability indirectly affected the NPP via stand biomass, while stand biomass had a significant direct effect on NPP regardless of whether the leaf water content and stand height were considered. The model based on stand size (71.6%) and the model that contained both stand size and water availability (72.3%) explained more of the variation in the water-NPP relationships than the model based on water availability (37.3%). Our findings suggest that even in extremely water-limited areas, the effects of water availability on plant growth and the kinetics of plant metabolism could be indirect via plant size, demonstrating the importance of plant size as an indicator of shrub productivity. This study explains the mechanisms underlying the NPP driving pattern and proposes a practical NPP model for arid ecosystems.
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http://dx.doi.org/10.1016/j.scitotenv.2019.133952DOI Listing
December 2019

Evaluation of Red Cell Distribution Width to Lymphocyte Ratio as Potential Biomarker for Detection of Colorectal Cancer.

Biomed Res Int 2019 31;2019:9852782. Epub 2019 Jul 31.

Department of Gastrointestinal Surgery, Guangxi Clinical Research Center for Colorectal Cancer, Affiliated Tumor Hospital, Guangxi Medical University, Nanning, Guangxi, China.

Background And Aim: Colorectal cancer (CRC) is the third most lethal cancer globally. This study sought to determine the feasibility of using red cell distribution width-to-lymphocyte ratio (RLR) as a tool to facilitate CRC detection.

Methods: Seventy-eight healthy controls, 162 patients diagnosed with CRC, and 94 patients with colorectal polyps (CP) from June 2017 to October 2018 were retrospectively reviewed. Clinical data were obtained to analyze preoperative RLR level, and receiver operating characteristic (ROC) curve analysis was performed to estimate the potential role of RLR as a CRC biomarker.

Results: RLR was higher in patients with CRC than in healthy participants ( < 0.05). ROC analysis indicated that combined detection of RLR and CEA appears to be a more effective marker to distinguish among controls, CP, and CRC patients, yielding 56% sensitivity and 90% specificity. RLR levels were significantly greater in those who had more advanced TNM stages ( < 0.05) and patients with distant metastasis stages ( < 0.05).

Conclusions: RLR might serve as a potential biomarker for CRC diagnosis.
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http://dx.doi.org/10.1155/2019/9852782DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6699340PMC
January 2020

A liver-specific lncRNA, FAM99B, suppresses hepatocellular carcinoma progression through inhibition of cell proliferation, migration, and invasion.

J Cancer Res Clin Oncol 2019 Aug 26;145(8):2027-2038. Epub 2019 Jun 26.

Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, 530021, Guangxi, People's Republic of China.

Background: Increasing evidence has shown that long non-coding RNAs (lncRNAs) are important in hepatocellular carcinoma (HCC) development and progression. In this study, we aim to evaluate the expression of lncRNA FAM99B and its biological function in HCC.

Methods: The expression level of FAM99B in HCC was assessed based on data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), verified using quantitative real-time polymerase chain reaction (qRT-PCR). HCCLM3 was transfected with lentivirus containing full-length FAM99B to obtain stable overexpressing cell line. Cell Counting Kit 8, clone formation, and transwell assays were used to investigate the effects of FAM99B in HCC progression. In addition, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and PANTHER pathway analyses were conducted to investigate the underlying molecular mechanisms.

Results: FAM99B was found to be downregulated in HCC tissues compared with adjacent normal tissues based on TCGA, GEO, and qRT-PCR data. Our results revealed that downregulated FAM99B was significantly associated with vascular invasion, advanced histologic grade, and T stage. Kaplan-Meier analysis using TCGA data indicated that decreased FAM99B levels were significantly associated with poor overall survival in patients with HCC. Moreover, overexpression of FAM99B significantly inhibited cell proliferation, migration, and invasion in vitro. Pathway analyses showed that the co-expressed genes of FAM99B mainly participated in the pathways "Metabolic pathways" and "Blood coagulation".

Conclusion: Our results suggest that FAM99B may serve as a tumor suppressor in HCC and may provide a promising therapy target for patients with HCC.
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http://dx.doi.org/10.1007/s00432-019-02954-8DOI Listing
August 2019